Ash's Secret History
by srebak
Summary: This is the secret history of the Pokemon Trainer Ash Ketchum. A history even he's mostly in the Dark about
1. Chapter 1

**Ash's Secret History: **

**Disclaimer:** I do not own Pokemon or anything from the TMNT franchise, this is purely fan fiction. I own nothing

When Ash Ketchum was merely 5 years old, his mother Delia enrolled him in an Elementary School-esque Prep school for children who enjoy Pokemon. Ash was there for sometime, but one day, he became the scapegoat to another student's prank, a prank that involved the principal and a Voltorb. After that, the poor boy was expelled from the school in disgrace. Ash was hurt, not only by the expulsion, but also by the fact that he was framed. Then one day, while he was out playing in the yard, he was approached by two strange looking men, in trench coats.

"Hello, young man" is what one said

Naturally, Ash remembered what his mother told him about talking to strangers. But before he could run back into the house, the second one grabbed him by his clothes and held high in the air. With that, the two mysterious men vanished, almost as mysteriously as they came.

Next thing Ash knew, he was on board a strange vehicle. Being as young as he was, Ash had no idea where he was, what he didn't know was that he was onboard a massive airship. All he knew was that he was in who knows how much trouble. Then, the doors to his room suddenly opened and Ash was approached by on of then men who took him.

"There, there, my boy, don't be afraid." He said while trying to pat Ash on the head.

Ash, still a little unsure about this man, backed up away from the man's hand.

Regardless, the man continued to speak "I know you must be wondering why you're here, my dear boy. But there is a simple reason for that, Mr. Ketchum"

This greatly throws Ash back. "How does he know my name? And what does he want from me?" he thought. All of this was so much to take in, so he sits himself down

"You see, I have been watching you for sometime now, ever since that horrible incident at your school. What that brat did to you was beyond unacceptable. But I think the main source of that problem would always be the same, no matter how you look at it; Pokemon!" The man continued

Ash was slightly more thrown by the last words of the sentence. He had always been interested in Pokemon and wanted to be a trainer. But on the other hand, Ash considered that if it weren't for that Voltorb, he probably wouldn't have been caught in that prank and gotten expelled in the first place.

"This is why I've brought you here, Ash, we're all of the same breed, you and I and my cohort here. We've all been hurt by those creatures and I for one am sick of it. Fortunately, we represent someone who can help you, like he has us."

Rather curious of what he meant exactly, Ash put up no further resistance as they approached a mountain range and entered a secret cavern. Once there, Ash and his "kidnappers" exited the vehicle and Ash got a good look at where he was, if a bit still unsure where he was. He had been brought to a massive secret base and as he was walked through the area, he saw a variety of strange things.

On one side, he saw up to twenty people, wearing ninja costumes performing jujitsu. On another, he saw more ninjas dragging in a variety of Pokemon out of another airship, all of them wearing some form of collars. When a Charizard tried to use flamethrower against them, nothing came out of its mouth and as retribution; one of the humans hit it with a large blue staff and shocked it. But what really caught Ash's eye was the massive picture that was painted in the very center of the base; a large, blood red, three-point trident.

"Uh, where are we? Who are you guys?" Ash asked, still rather bewildered

"Ash, welcome to the Foot, for years our little club has had one thing in common, we've all been wronged by Pokemon. Those monsters have had their way with our world for too long. They're too powerful, and with that power, they're beyond dangerous. The Foot clan was formed to protect the world from those creatures" his "Tour Guide" answered

Ash a little unsure about that, he was always taught that Pokemon and humans should be able live together. But now, being brought before people against Pokemon, his views began to grow more unclear, especially at this early in his development.

Ash was given a further tour of the base and was amazed and unsettled by what lied within it. He was brought to the Foot's labs, where they performed rather unpleasant tests and experiments of Pokemon, and was introduced to the organization's scientists, namely the head scientist, Baxter Stockman.

The tour then brought Ash to the training facilities and Armories, where he met two of the Foot's high ranking members; Hun and General Smytus, neither of which were too happy about him being here.

Finally, Ash was brought to the very heart of the Foot's HQ, the office of the organization's leader, Oroku Saki.

The strangely dressed man welcomed Ash and began to have a talk with him. Saki claims that he sympathizes with what Ash has gone through and says that the best way to truly get over it is to get even. Saki offers Ash a chance to exact revenge on all those who wronged him. And all Ash would have to do, is agree to help Stockman in his most recent experiment.

Ash was unsure about this, but he was still relatively angry over what happened at his school and wanted revenge for it. So, he accepted Saki's offer. Ash was then led back to the Foot Clan Labs and Baxter Stockman prepared him for the experiment. The idea was to find a way to enhance the strength, agility and intelligence, and Stockman had created it. A special type of serum that, once injected, will give a small child like Ash the strength and power of a full grown Ninja master, and if the serum would have that effect on a child, the possibilities for an adult would be very exceptional.

Ash was placed into a test tube and was injected with Stockman's serum via his skin. When the process was over, Ash's muscles may have looked unchanged, but their power was increased 20 fold and his brain capacity was increased by 50%. But what really seemed like the biggest side effect was that Ash had developed an evil streak.

After that day, Ash served under the Foot, as a field operative and as an example of the serum's effectiveness, which Stockman continued to administer to the younger Foot Clan trainees.

With his new evil streak Ash felt more interested than ever in getting revenge, which he did, in a very violent way. What's more, Ash was far too malevolent and far too sociopathic, that he didn't even care about discovering the truth about the Foot Clan. True, the Foot wishes to "protect" the world from Pokemon, but they think the only way to do so, is to rid the Earth of all Pokemon. What's more, he is also informed that the Foot has another goal, conquering the Earth as far as the eye can see. All in the name of Oroku Saki, who Ash learns goes by another name, The Shredder.

Over the months, Saki watched Ash's skills improve and felt he could use someone of his skills in a higher rank. After being a field operative, Ash was promoted to overseeing certain Foot clan operations. Then he was assigned to helping train Foot clan recruits, during his time doing this, he actually made a select few into a group of fearsome ninjas who are now known as the Foot Clan Elite. Eventually, Ash was promoted to Saki's High Command, his most trusted minions, the rest of the High Command included Smytus, Hun, Stockman and the Shredder's adopted daughter, Karai. They could be considered an evil version of the Elite Four.

As one of Saki's most trusted warriors, Ash was given access to many of the organization's troops and resources (all of which were rather unusual for a toddler to have possession of). He was also responsible for overseeing the Foot's operations in the Kanto region and therefore was responsible for a large number of crimes and damage done by the Foot Ninjas.

The Foot Clan is able to do so much damage because they have sunk their claw into the very government itself. Not many police are willing to arrest them (because some Officer Jenny's are members) and not many courts can try or hold them if they were arrested. While The Shredder doesn't completely have control, the Foot Clan does appear to be in more power than Team Rocket (who also subsequently serve under for the Foot Clan, if only a little bit).

Every now and then, Ash would briefly snap out of his evil frenzies and remember his family. Fearing that this would make him lose control over his new soldier, the Shredder had his ninjas go out and retrieve one of Ash's family members. To better keep anyone from looking for him, the Foot clan used special technology to almost erase any memory of Ash's existence from Pallet Town, thus keeping anyone from looking for him when he was first recruited. But now, they returned to Pallet Town and brought back another Ketchum, Ash's sister, Elsa.

Like what happened to Ash, the Foot had Elsa's very identity erased from the minds of Pallet Town. When she was brought to Foot HQ, she was put through the same process as Ash and became a living weapon like him. But the process had an unusual effect on her right arm. As a result, she was given a bio-mechanical replacement.

Together, the Ketchum Siblings were two of the Foot Clan's fiercest agents, which is saying something, considering they were still less than the required age for training Pokemon, let alone hunting them. But because the serum that flowed within them made them so aggressive and evil, they both began to prove to be far too evil and aggressive to control. Since simply having the two eliminated would prove wasteful in the long run, the Foot instead decided to have their memories wiped. Ash and Elsa were apprehended and were both stripped of their memories of their time as Foot Clan operatives.

Ash was returned to his home in Pallet, since the Shredder believed that Ash would pose no threat in the long run. But Elsa accidentally stumbled off before she was returned home and was left out on her own, bereft. As such, with Elsa missing in action, for some time it was believed that Ash had no sister, though vague memories of her came and went until they finally met again in Johto.

For some time now, the Foot continued its evil operations without Ash; the Shredder himself regards the issue with him as a minor bump in the road. Unfortunately, in a few years time, Ash became a Pokemon trainer and returned to one of the towns that the Foot occupy. After interfering with the Foot's operations there, Ash, his Pokemon and his friends have made a habit of interfering in Foot Clan business and shutting them down. What's more Ash is slowly becoming more and more aware of his past atrocities. But that only makes him more interested in bring down the Foot for what they do to Pokemon.

**The Foot of the Problem**

(Takes place during the Johto Saga)

(I own nothing from Pokemon or TMNT)

As Ash and co. continue their journey through Johto, they arrive at a nearby town, only to find it practically abandoned. All of a sudden, Misty thinks she saw something nearby and Brock thinks he saw it too. Ash looks another direction, claiming he saw something nearby there, Pikachu claims it saw it too. Finally, Persian sees something, only this time it was right in front of him. In seconds, the whole group sees what the talking Pokemon sees, a man wearing what looked like a ninja uniform. They are shocked by this, even more so when they see what he is carrying, a long spear-like staff. Suddenly, Pikachu hears something from several different directions and everyone comes to sees that they're surrounded, by 7 more people wearing the exact same uniform and carrying the same weapon as the first guy.

Upon further inspection of their uniforms, Ash and Co. clearly see that these people aren't with Team Rocket. (Instead of a big red R, these men all have a red, three-pointed Trident shape as their logo). What's more, as Ash inspects them, he can't help but feel like he's seen them before. When they all demand that they reveal who they really are, none of them say a word; instead, they all attack en masse. Ash then sends in Pikachu and calls out Chikorita and Cyndaquil for assistance. Misty and Brock join in with Geodude and Staryu as well.

But before any attacks could be used, one of these ninjas raised his staff and pressed a button on it. Then the tip began to glow with what appeared to be red energy. Then, he aimed it at Pikachu and fired what looked like collar of red energy. When it finally got around Pikachu's neck, the ninja fired 5 more and they were soon around the necks of all of the Pokemon, except Togepi.

When Pikachu tries to use Thunderbolt, nothing happened, not even a crackle of electricity. The same thing happened with every other Pokemon wearing these red collars, they tried to use an attack, but nothing happened. Except Geodude, its energy collar only kept it from moving. With their opponents rendered powerless, the other ninjas use their staffs to blast the neutralized Pokemon.

Persian and Pikachu were the only ones to get back up, but before they could try to attack, one of the ninjas presses another button on his staff and makes the collars on them glow. Suddenly, the two Pokemon are dealt a high voltage shock that brings them both collapsing to the ground.

As the ninjas advanced further towards the trainers, Officer Jenny rides up and has Arcanine uses flamethrower which chases the ninjas away. After getting the collars off, the policewoman escorts the trainers to the nearest Pokemon Center. While the Pokemon are treated, Officer Jenny tells Ash and Co. that they were attacked by a group that has a reputation for hunting Pokemon. While the kids are disgusted by this, Ash has continued to have the strange feelings he had about those men. Though he doesn't know why, something about them seemed familiar.

Meanwhile, Team Rocket is still on the trail of Ash and Co. and all three are quite exhausted from all the walking. Then, like our heroes, they are ambushed by the mysterious group of Ninjas. Naturally, in an attempt to seem important, they call out Wheezing and Arbok to battle. But naturally, they're defeated quite easily. After that, they attempt to retreat, but are cut off by two of the Ninjas.

Then, the biggest of the ninjas walks up to them and grabs Jessie and James by their collars and hoists them up. And after pulling them closer to him, he actually speaks and in a rather intimidating voice at that. He tells the two whimpering TR agents

"Tell your precise boss that the next time Team Rocket comes into our territory, there will be no more Team Rocket!"

After that, the leader drops the TR agents, then he and all the other ninjas vanish without a trace. Leaving Jessie, James and Meowth still shaking in fear of what just happened. Meanwhile, back at the Pokemon Center, Ash, Misty and Brock are overjoyed to know that their Pokemon are all making quick recoveries. Then, they all tell Officer Jenny that they want to help her catch these Pokemon hunters. But while this conversation is taking place, one of the ninjas from before is in disguise at the PC and is listening in on their conversation. But suddenly, when he hears Ash's voice and name, he is shocked and runs off for some reason.

The Ninja moves quickly until he reaches the outside forest. There, he proceeds to a cliff side and places his hand on a rock, which is revealed to actually be a button. Suddenly, a secret door opens and the mysterious man enters and is taken underground via elevator. Deep underground, there is a massive complex, filled high tech weaponry and vehicles, and with the same men who attacked Ash and co. and TR. All of them are wearing the Red-trident insignia and all of them carry the same type of weapon.

As the spy continues through the complex, he finally arrives at a massive video screen. After turning it on, he contacts a man who could be considered the leader of these men. He then informs him that

"Ash is back".

Those words hit the leader like a 2X4 upside the head. He then orders his spy to carry on his work and to inform the others that he will be visiting their base soon. After hanging up, the spy obeys his boss' orders and informs his fellow ninjas. As they all rally, they all stand erect and recite the oath of their little group.

"**We are the Superior Breed**

**We are the future of Mankind**

**All Pokemon are our enemies**

**And must be wiped off the face of the Earth**

**For we are Fighters**

**We are Warriors**

**We are the Foot Clan!"**

Meanwhile, the leader is revealed to have gotten that call while riding in a helicopter that puts Giovanni's to shame. He then says to himself

"So, Ash has resurfaced has he? The boy obviously couldn't leave well enough alone. Well, at the very least, we have been given the chance to either regain a lost member of our family, or to put an end to a long forgotten mistake!"

**To Be Continued**

Swords and Secrets:

(Takes place during the Johto Saga)

(I own nothing from Pokemon or TMNT)

After being attacked by a mysterious group of Pokemon hunting ninjas, Ash, Misty, Brock and Persian all set out to help Officer Jenny catch them before they're able to hurt anyone else. Ash and Brock send out Noctowl and Golbat to patrol the area from the sky, while everyone else joins Officer Jenny in her jeep, searching for any sign of the enemy.

But while they were riding around, they were being watched by two more of said ninjas. But unlike the ones from before, these two were wearing a special type of suit that actually made them invisible. One of them then speaks into a communicator and reports back to his base commander:

"Master, we've located the target, but he's with the local authorities."

"Wait until he's alone, then you can proceed to take him. Then, report back to base when you do"

"Yes Master"

Per their given orders, the two ninjas proceed to follow our heroes, in camouflage mode of course. But rather than wait until anyone was alone, one of the ninjas went in one direction and made enough noise and commotion to attract the attention of our heroes. Then, when everyone was distracted, the other came up from behind and tossed several strange looking spheres. When they were under everyone's feet, each of the spheres releases a powerful electric jolt, ala Voltorb.

This was more than enough to stun everyone long enough for the other ninja to fire a stringy substance, very similar to Spinarak and Ariados' web, which wraps up everyone, human and Pokemon. And as everyone struggled to get free, the two ninjas regroup and practically disappear into the trees, with Ash in tow.

When they're gone, Persian manages to free himself and everyone else. Misty and Brock are both shocked about Ash being kidnapped and concerned about why he was kidnapped. But most importantly, worried about what will befall their friend.

Meanwhile, the leader of these Pokemon hunters, the Foot Clan as they call themselves, has just arrived at their Cliffside base by helicopter. Once there, he is given a fabulous and respected welcome, he is also soon greeted by the base commander:

"Oroku Saki, lord and master of the Foot Clan. I welcome you to my Base, my lord"

"Enough fanfare, Koran, I was told that our old friend, Ash Ketchum, has resurfaced and is apparently sticking his nose where doesn't belong"

"Indeed Master, I've dispatched two ninjas to follow and apprehend him"

"Excellent, then once they have him here, we can take care of things, as it were"

And with that, Koran bows in respect to his leader. But what none of the Foot ninja knew, was that the TR trio was nearby their base and saw Saki's helicopter as it came in. They started looking around, but eventually, they were spotted and the Foot sounded the alarm. Jessie and James panic, until Meowth finally tells them to run. But even though they manage to get far enough away before the guards show up, the same ninja who confronted them before walks up and says:

"I warned those clowns, Team Rocket is going to pay for this, big time!"

Meanwhile, back inside the base, Oroku Saki and Koran had watched the security cameras and saw what just happened. But their attention was drawn away when the doors behind them suddenly open. It was the same two ninjas that attacked our heroes earlier, and they still had Ash tow, tied up and now gagged. They then place him on his knees and present him before Saki himself. Saki then proceeds to talk to Ash as he removes his gag:

"Well, well, well, Ash Ketchum, it's been a long time"

Once the gag was off, Ash attempts to talk

"Hey, who do you think you…Hey how do you know my name?"

"(Chuckles) I should've known you wouldn't remember. But not to worry, we'll fix that soon enough"

As Saki attempts to pat Ash on his head, but the young trainer just pulls his head away in disgust.

"(Chuckles) Still as spunky as ever, I see. (Turns towards the two Foot Ninjas) Take him to the lab; we'll begin the procedure, right away"

And with that, the two ninjas pick Ash up and carry him off, with Saki and Koran following them. Meanwhile, Misty, Brock, Pikachu and Persian were searching desperately for any trace of the ninjas, hoping to find something that may lead them to Ash. Officer Jenny even called out her Arcanine to help with the search. But even with Arcanine's sense of smell, they still weren't finding anything.

Suddenly, Golbat and Noctowl return from their search and try to report what they found. Persian translates that they saw a strange looking helicopter with the Ninjas' symbol on it. They saw it heading for a nearby Cliffside, almost as if it were going to land. This was reason enough to investigate, especially if it meant finding and rescuing Ash. So the rest of the group followed Noctowl and Golbat as they led them to the cliff side.

Meanwhile, back at the Foot Clan base, Oroku Saki had Ash taken to the base's laboratory and placed in some sort of examination table. There, three scientists looked at him as he struggled to get free, all of them with facial expressions indicating that they were about to do something unpleasant, particularly the scientist who looked like he was the one in charge.

"Dr. Stockman, are you ready to proceed?"

"Indeed, Master Saki, I've done experiments on Ash before, I'll do it again. When I'm through, all he'll know is that he belongs to the Foot, now and forever"

After that, Stockman has his fellow scientists take Ash's hat off and place a technological looking headband on his head. Suddenly, Ash felt faint and slowly began to fall asleep. Then, he heard Oroku Saki begin to tell him a story about his life. He tells Ash that he was once a member of the Foot Clan organization and Right-hand man to Saki himself. Ash was a volunteer in a previous experiment of Stockman, where he was augmented by a secret serum that not only enhanced his natural abilities, but also gave some rather unnatural ones as well. What's more, it also gave him an evil streak.

When Ash heard this, he was both disgusted and ashamed. For so long, he's always considered himself a friend to Pokemon, but now, he finds that he was once their enemy. As Ash gave the facial expression of disgrace, Stockman removed the headband and had the other scientists remove him from the table. Then Saki walks over to Ash, pats him on the head and says:

"There, There, Ash, it won't matter. Like Stockman said, soon all you'll remember is that you belong to me!"

After that, Stockman and the other scientists drag Ash off and place him in a strange looking chair, almost like an electric chair. But before they could properly strap him in, one of the Foot Ninja came running in.

"Master, we have intruders, it's that pest, Officer Jenny"

"Is that so?"

"Yes and there's more, sir, she's with those people we found with Ketchum here"

That bit of information suddenly perked Ash up a bit, but Saki just smiles and says:

"So, a rescue is it, we can fix that"

Meanwhile, outside, Golbat and Noctowl had led Misty, Brock, Jenny, Pikachu and Persian to the exact Cliffside where they saw the helicopter fly towards. But just when they were about to look around for anything helpful, several Foot Ninja wearing camouflage suits appear out of nowhere and toss several of the shocking spheres from before, all around their feet. Then, before anyone knew it, they were all shocked and rendered unconscious. That's when Oroku Saki came onto the scene, but this time, he was in shadow and the silhouette he was casting gave the impression he was wearing some sort of suit. And all that was heard from him was a maniacal laugh.

**TO BE CONTINUED **


	2. Chapter 2

**The Foot of the Problem**

(Takes place during the Johto Saga)

(I own nothing from Pokemon or TMNT)

As Ash and co. continue their journey through Johto, they arrive at a nearby town, only to find it practically abandoned. All of a sudden, Misty thinks she saw something nearby and Brock thinks he saw it too. Ash looks another direction, claiming he saw something nearby there, Pikachu claims it saw it too. Finally, Persian sees something, only this time it was right in front of him. In seconds, the whole group sees what the talking Pokemon sees, a man wearing what looked like a ninja uniform. They are shocked by this, even more so when they see what he is carrying, a long spear-like staff. Suddenly, Pikachu hears something from several different directions and everyone comes to sees that they're surrounded, by 7 more people wearing the exact same uniform and carrying the same weapon as the first guy.

Upon further inspection of their uniforms, Ash and Co. clearly see that these people aren't with Team Rocket. (Instead of a big red R, these men all have a red, three-pointed Trident shape as their logo). What's more, as Ash inspects them, he can't help but feel like he's seen them before. When they all demand that they reveal who they really are, none of them say a word; instead, they all attack en masse. Ash then sends in Pikachu and calls out Chikorita and Cyndaquill for assistance. Misty and Brock join in with Geodude and Staryu as well.

But before any attacks could be used, one of these ninjas raised his staff and pressed a button on it. Then the tip began to glow with what appeared to be red energy. Then, he aimed it at Pikachu and fired what looked like collar of red energy. When it finally got around Pikachu's neck, the ninja fired 5 more and they were soon around the necks of all of the Pokemon, except Togepi.

When Pikachu tries to use Thunderbolt, nothing happened, not even a crackle of electricity. The same thing happened with every other Pokemon wearing these red collars, they tried to use an attack, but nothing happened. Except Geodude, its energy collar only kept it from moving. With their opponents rendered powerless, the other ninjas use their staffs to blast the neutralized Pokemon.

Persian and Pikachu were the only ones to get back up, but before they could try to attack, one of the ninjas presses another button on his staff and makes the collars on them glow. Suddenly, the two Pokemon are dealt a high voltage shock that brings them both collapsing to the ground.

As the ninjas advanced further towards the trainers, Officer Jenny rides up and has Arcanine uses flamethrower which chases the ninjas away. After getting the collars off, the policewoman escorts the trainers to the nearest Pokemon Center. While the Pokemon are treated, Officer Jenny tells Ash and Co. that they were attacked by a group that has a reputation for hunting Pokemon. While the kids are disgusted by this, Ash has continued to have the strange feelings he had about those men. Though he doesn't know why, something about them seemed familiar.

Meanwhile, Team Rocket is still on the trail of Ash and Co. and all three are quite exhausted from all the walking. Then, like our heroes, they are ambushed by the mysterious group of Ninjas. Naturally, in an attempt to seem important, they call out Wheezing and Arbok to battle. But naturally, they're defeated quite easily. After that, they attempt to retreat, but are cut off by two of the Ninjas.

Then, the biggest of the ninjas walks up to them and grabs Jessie and James by their collars and hoists them up. And after pulling them closer to him, he actually speaks and in a rather intimidating voice at that. He tells the two whimpering TR agents

"Tell your precise boss that the next time Team Rocket comes into our territory, there will be no more Team Rocket!"

After that, the leader drops the TR agents, then he and all the other ninjas vanish without a trace. Leaving Jessie, James and Meowth still shaking in fear of what just happened. Meanwhile, back at the Pokemon Center, Ash, Misty and Brock are overjoyed to know that their Pokemon are all making quick recoveries. Then, they all tell Officer Jenny that they want to help her catch these Pokemon hunters. But while this conversation is taking place, one of the ninjas from before is in disguise at the PC and is listening in on their conversation. But suddenly, when he hears Ash's voice and name, he is shocked and runs off for some reason.

The Ninja moves quickly until he reaches the outside forest. There, he proceeds to a cliff side and places his hand on a rock, which is revealed to actually be a button. Suddenly, a secret door opens and the mysterious man enters and is taken underground via elevator. Deep underground, there is a massive complex, filled high tech weaponry and vehicles, and with the same men who attacked Ash and co. and TR. All of them are wearing the Red-trident insignia and all of them carry the same type of weapon.

As the spy continues through the complex, he finally arrives at a massive video screen. After turning it on, he contacts a man who could be considered the leader of these men. He then informs him that

"Ash is back".

Those words hit the leader like a 2X4 upside the head. He then orders his spy to carry on his work and to inform the others that he will be visiting their base soon. After hanging up, the spy obeys his boss' orders and informs his fellow ninjas. As they all rally, they all stand erect and recite the oath of their little group.

"**We are the Superior Breed**

**We are the future of Mankind**

**All Pokemon are our enemies**

**And must be wiped off the face of the Earth**

**For we are Fighters**

**We are Warriors**

**We are the Foot Clan!"**

Meanwhile, the leader is revealed to have gotten that call while riding in a helicopter that puts Giovanni's to shame. He then says to himself

"So, Ash has resurfaced has he? The boy obviously couldn't leave well enough alone. Well, at the very least, we have been given the chance to either regain a lost member of our family, or to put an end to a long forgotten mistake!"

**To Be Continued**


	3. Chapter 3

**Swords and Secrets:**

**(Takes place during the Johto Saga)**

**(I own nothing from Pokemon or TMNT)**

After being attacked by a mysterious group of Pokemon hunting ninjas, Ash, Misty, Brock and Persian all set out to help Officer Jenny catch them before they're able to hurt anyone else. Ash and Brock send out Noctowl and Golbat to patrol the area from the sky, while everyone else joins Officer Jenny in her jeep, searching for any sign of the enemy.

But while they were riding around, they were being watched by two more of said ninjas. But unlike the ones from before, these two were wearing a special type of suit that actually made them invisible. One of them then speaks into a communicator and reports back to his base commander:

"Master, we've located the target, but he's with the local authorities."

"Wait until he's alone, then you can proceed to take him. Then, report back to base when you do"

"Yes Master"

Per their given orders, the two ninjas proceed to follow our heroes, in camouflage mode of course. But rather than wait until anyone was alone, one of the ninjas went in one direction and made enough noise and commotion to attract the attention of our heroes. Then, when everyone was distracted, the other came up from behind and tossed several strange looking spheres. When they were under everyone's feet, each of the spheres releases a powerful electric jolt, ala Voltorb.

This was more than enough to stun everyone long enough for the other ninja to fire a stringy substance, very similar to Spinarak and Ariados' web, which wraps up everyone, human and Pokemon. And as everyone struggled to get free, the two ninjas regroup and practically disappear into the trees, with Ash in tow.

When they're gone, Persian manages to free himself and everyone else. Misty and Brock are both shocked about Ash being kidnapped and concerned about why he was kidnapped. But most importantly, worried about what will befall their friend.

Meanwhile, the leader of these Pokemon hunters, the Foot Clan as they call themselves, has just arrived at their Cliffside base by helicopter. Once there, he is given a fabulous and respected welcome, he is also soon greeted by the base commander:

"Oroku Saki, lord and master of the Foot Clan. I welcome you to my Base, my lord"

"Enough fanfare, Koran, I was told that our old friend, Ash Ketchum, has resurfaced and is apparently sticking his nose where doesn't belong"

"Indeed Master, I've dispatched two ninjas to follow and apprehend him"

"Excellent, then once they have him here, we can take care of things, as it were"

And with that, Koran bows in respect to his leader. But what none of the Foot ninja knew, was that the TR trio was nearby their base and saw Saki's helicopter as it came in. They started looking around, but eventually, they were spotted and the Foot sounded the alarm. Jessie and James panic, until Meowth finally tells them to run. But even though they manage to get far enough away before the guards show up, the same ninja who confronted them before walks up and says:

"I warned those clowns, Team Rocket is going to pay for this, big time!"

Meanwhile, back inside the base, Oroku Saki and Koran had watched the security cameras and saw what just happened. But their attention was drawn away when the doors behind them suddenly open. It was the same two ninjas that attacked our heroes earlier, and they still had Ash tow, tied up and now gagged. They then place him on his knees and present him before Saki himself. Saki then proceeds to talk to Ash as he removes his gag:

"Well, well, well, Ash Ketchum, it's been a long time"

Once the gag was off, Ash attempts to talk

"Hey, who do you think you…Hey how do you know my name?"

"(Chuckles) I should've known you wouldn't remember. But not to worry, we'll fix that soon enough"

As Saki attempts to pat Ash on his head, but the young trainer just pulls his head away in disgust.

"(Chuckles) Still as spunky as ever, I see. (Turns towards the two Foot Ninjas) Take him to the lab; we'll begin the procedure, right away"

And with that, the two ninjas pick Ash up and carry him off, with Saki and Koran following them. Meanwhile, Misty, Brock, Pikachu and Persian were searching desperately for any trace of the ninjas, hoping to find something that may lead them to Ash. Officer Jenny even called out her Arcanine to help with the search. But even with Arcanine's sense of smell, they still weren't finding anything.

Suddenly, Golbat and Noctowl return from their search and try to report what they found. Persian translates that they saw a strange looking helicopter with the Ninjas' symbol on it. They saw it heading for a nearby Cliffside, almost as if it were going to land. This was reason enough to investigate, especially if it meant finding and rescuing Ash. So the rest of the group followed Noctowl and Golbat as they led them to the cliff side.

Meanwhile, back at the Foot Clan base, Oroku Saki had Ash taken to the base's laboratory and placed in some sort of examination table. There, three scientists looked at him as he struggled to get free, all of them with facial expressions indicating that they were about to do something unpleasant, particularly the scientist who looked like he was the one in charge.

"Dr. Stockman, are you ready to proceed?"

"Indeed, Master Saki, I've done experiments on Ash before, I'll do it again. When I'm through, all he'll know is that he belongs to the Foot, now and forever"

After that, Stockman has his fellow scientists take Ash's hat off and place a technological looking headband on his head. Suddenly, Ash felt faint and slowly began to fall asleep. Then, he heard Oroku Saki begin to tell him a story about his life. He tells Ash that he was once a member of the Foot Clan organization and Right-hand man to Saki himself. Ash was a volunteer in a previous experiment of Stockman, where he was augmented by a secret serum that not only enhanced his natural abilities, but also gave some rather unnatural ones as well. What's more, it also gave him an evil streak.

When Ash heard this, he was both disgusted and ashamed. For so long, he's always considered himself a friend to Pokemon, but now, he finds that he was once their enemy. As Ash gave the facial expression of disgrace, Stockman removed the headband and had the other scientists remove him from the table. Then Saki walks over to Ash, pats him on the head and says:

"There, There, Ash, it won't matter. Like Stockman said, soon all you'll remember is that you belong to me!"

After that, Stockman and the other scientists drag Ash off and place him in a strange looking chair, almost like an electric chair. But before they could properly strap him in, one of the Foot Ninja came running in.

"Master, we have intruders, it's that pest, Officer Jenny"

"Is that so?"

"Yes and there's more, sir, she's with those people we found with Ketchum here"

That bit of information suddenly perked Ash up a bit, but Saki just smiles and says:

"So, a rescue is it, we can fix that"

Meanwhile, outside, Golbat and Noctowl had led Misty, Brock, Jenny, Pikachu and Persian to the exact Cliffside where they saw the helicopter fly towards. But just when they were about to look around for anything helpful, several Foot Ninja wearing camouflage suits appear out of nowhere and toss several of the shocking spheres from before, all around their feet. Then, before anyone knew it, they were all shocked and rendered unconscious. That's when Oroku Saki came onto the scene, but this time, he was in shadow and the silhouette he was casting gave the impression he was wearing some sort of suit. And all that was heard from him was a maniacal laugh.

**TO BE CONTINUED**


End file.
